Right, what I'm asking about is<div>A) how exactly is this end result <span></span>achieved? (The system is periodic, so how is the periodicity removed for the end state?)</div><div>B) how was it validated that it is working as it should be?</div>
<div>C) when you say, "without cutoffs", is this referring to just Coulomb cutoffs or also LJ? I'm assuming just coulomb. If so, then there are internal LJ interactions in the gas phase which are missing outside the LJ cutoff (assuming the molecule is larger than the cutoff). While these are also missing in solution, they are generally captured well by the dispersion correction. In vacuum that is not the case, so neglect of these could adversely affect solvation estimates, it seems to me. Has this been tested? How?</div>
<div>D) how will the use of decoupling affect dispersion corrections to the energy and pressure? (Will the dispersion corrections still give the correct free energy contribution in decoupling?) how has this been tested, if at all?</div>
<div><br></div><div>Thanks!<br><br>On Thursday, May 2, 2013, Berk Hess wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi,<br>
<br>
You didn't explain exactly what you are doing.<br>
The decouple mdp options decouple the molecule to a vacuum state,
i.e. pure Coulomb without cut-off's.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 05/02/2013 07:10 PM, David Mobley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Could I get some input on this?<br>
<br>
I have a couple of cases for rather polar molecules where
decoupling and annihilation give me statistical significant
differences in hydration free energies. The differences are not
that large, but significant. I'm trying to find out what's
already been done to validate so I know how much time/effort to
spend testing to try and figure out if there is a problem here.<br>
<br>
Thanks.</div>
<div><br>
<br>
<div>On Tue, Apr 30, 2013 at 1:25 PM, David
van der Spoel <span dir="ltr"><<a>spoel@xray.bmc.uu.se</a>></span>
wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 2013-04-30 18:02, David Mobley wrote:<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
In GROMACS 4.6 and later, there's now a new feature
available to allow<br>
decoupling of solute molecules in free energy
calculations. I wanted to<br>
inquire as to how Coulomb decoupling works, as I'm not
clear.<br>
<br>
Specifically, imagine I'm running a calculation of the
hydration free<br>
energy of a small molecule in water, and I decouple it
(LJ and Coulomb)<br>
from its surroundings. What is the final reference state
for the small<br>
molecule? Is it the small molecule interacting with
periodic copies of<br>
itself in the gas phase (bad)? Or is it not interacting
with periodic<br>
copies of itself either? If the latter, how is this
achieved?<br>
</blockquote>
</div>
Good question, also one would like to be able to decouple a
molecule only in the central box and not in the surrounding
boxes. This does not make a difference for liquids but it
does for crystals.<br>
<blockquote style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<br>
Since I'm not familiar with the Coulomb decoupling
aspect and it is<br>
conceptually more complicated than LJ decoupling, I want
to make sure I<br>
understand how it's supposed to be working.<br>
<br>
Thanks!<br>
David<br>
<br>
<br>
--<br>
David Mobley<br>
</div>
<a>dmobley@gmail.com</a> <mailto:<a>dmobley@gmail.com</a>><br>
<a value="+19493852436">949-385-2436</a><br>
<br>
<br>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a value="+46184714205">+46184714205</a>.<br>
<a>spoel@xray.bmc.uu.se</a>
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</div>
<br>
<br clear="all">
<br>
-- <br>
David Mobley<br>
<a></a></div></blockquote></div>
</blockquote></div><br><br>-- <br>Sent from my mobile device. Please pardon any unusual brevity or typos. <br>